rs4233356

Variant names:

• chr1-159783393-A-G
• rs4233356

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.634 in 152,094 control chromosomes in the GnomAD database, including 30,758 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (30758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96354 AN: 151976 Hom.: 30729 Cov.: 33

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.634 AC: 96424 AN: 152094 Hom.: 30758 Cov.: 33 AF XY: 0.642 AC XY: 47728 AN XY: 74348

African (AFR) AF: 0.594 AC: 24627 AN: 41468

American (AMR) AF: 0.649 AC: 9925 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3662 AN: 5158

South Asian (SAS) AF: 0.689 AC: 3324 AN: 4824

European-Finnish (FIN) AF: 0.749 AC: 7921 AN: 10572

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43083 AN: 67990

Other (OTH) AF: 0.587 AC: 1239 AN: 2112

Alfa AF: 0.631 Hom.: 141066

Bravo AF: 0.623

Asia WGS AF: 0.684 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		0.033

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4233356; hg19: chr1-159753183;